Introduction to CBioPortal

Research Fellow
Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute

• CBioPortal overview
• Data retrieval from CBioPortal using cgdsr
  • List cancer datasets
  • List data types for dataset
  • List case sets
  • Retrieve data for selected genes
  • Retrieve clinical data
• Plotting retrieved data

• Interactive Website: http://www.cbioportal.org/
• Project provides an application programming interface (API)
  • Makes CBioPortal accessible from any programming language
  • http://www.cbioportal.org/web_api.jsp
• cgdsr R Package simplifies access to the CBioPortal API

• NOTE: Not all samples will have complete data
  • DNA copy number variation
  • mRNA expression
  • microRNA expression
  • Mutation profiles
  • Protein and phosopho-protein expression
  • DNA methylation
  • Limited de-identified clinical data

• Notes on the available data
  • http://www.cbioportal.org/faq.jsp
• Example notes
  • Clinical data, includes: overall and disease-free survival, gender, age, stage and tumor grade, when available.
  • mRNA and microRNA data is z-scored (i.e. the number of standard deviations away from the mean of expression

• CBioPortal Google Group
  • http://groups.google.com/group/cbioportal
• Biostars
  • https://www.biostars.org/t/cbioportal/